Identifying reaction modules in metabolic pathways: bioinformatic deduction and experimental validation of a new putative route in purine catabolism

BMC Syst Biol. 2013 Oct 5;7:99. doi: 10.1186/1752-0509-7-99.

Abstract

Background: Enzymes belonging to mechanistically diverse superfamilies often display similar catalytic mechanisms. We previously observed such an association in the case of the cyclic amidohydrolase superfamily whose members play a role in related steps of purine and pyrimidine metabolic pathways. To establish a possible link between enzyme homology and chemical similarity, we investigated further the neighbouring steps in the respective pathways.

Results: We identified that successive reactions of the purine and pyrimidine pathways display similar chemistry. These mechanistically-related reactions are often catalyzed by homologous enzymes. Detection of series of similar catalysis made by succeeding enzyme families suggested some modularity in the architecture of the central metabolism. Accordingly, we introduce the concept of a reaction module to define at least two successive steps catalyzed by homologous enzymes in pathways alignable by similar chemical reactions. Applying such a concept allowed us to propose new function for misannotated paralogues. In particular, we discovered a putative ureidoglycine carbamoyltransferase (UGTCase) activity. Finally, we present experimental data supporting the conclusion that this UGTCase is likely to be involved in a new route in purine catabolism.

Conclusions: Using the reaction module concept should be of great value. It will help us to trace how the primordial promiscuous enzymes were assembled progressively in functional modules, as the present pathways diverged from ancestral pathways to give birth to the present-day mechanistically diversified superfamilies. In addition, the concept allows the determination of the actual function of misannotated proteins.

Publication types

  • Research Support, Non-U.S. Gov't
  • Validation Study

MeSH terms

  • Carboxyl and Carbamoyl Transferases / metabolism
  • Computational Biology / methods*
  • Dihydroorotate Dehydrogenase
  • Dihydrouracil Dehydrogenase (NADP) / metabolism
  • Glycine / analogs & derivatives
  • Glycine / metabolism
  • Metabolic Networks and Pathways*
  • Oxidoreductases Acting on CH-CH Group Donors / metabolism
  • Phylogeny
  • Purines / metabolism*
  • Urea / analogs & derivatives
  • Urea / metabolism

Substances

  • Dihydroorotate Dehydrogenase
  • Purines
  • ureidoglycine
  • Urea
  • Oxidoreductases Acting on CH-CH Group Donors
  • Dihydrouracil Dehydrogenase (NADP)
  • Carboxyl and Carbamoyl Transferases
  • Glycine
  • purine